Product Version = NetBeans IDE 7.1.1 (Build 201203012225)
Operating System = Linux version 3.0.0-16-generic running on i386
Java; VM; Vendor = 1.6.0_26
Runtime = Java HotSpot(TM) Client VM 20.1-b02
When executing a long running SQL query, an attempt to cancel the running query (clicking "X" in the status bar) does not do anything. Even after restarting the mySql service, the "Executing SQL statement(s)" progress bar is still hanging in the status bar. Still, the CPU seems to be running on 50%. Only restarting the IDE will set back to normal.

You are right - this is a long standing issue (and today a collegue was biten by this bug). The issue is not 100% the same, but the cause is (not being able to cancel a statement correctly). For hanging at 50% CPU seems to be another issue or a bug in the underlying jdbc driver.
*** This bug has been marked as a duplicate of bug 159929 ***